Metabolite Production in Endophytes

ABSTRACT

The present invention relates to nucleic acids encoding amino acid sequences for the biosynthesis of janthitrem in janthitrem producing endophytes. The present invention also relates to constructs and vectors including such nucleic acids, and related polypeptides, regulatory elements and methods.

FIELD OF THE INVENTION

The present invention relates to the biosynthesis of janthitremcompounds. In particular, the invention relates to genes encodingenzymes responsible for the synthesis of janthitrem and relatedconstructs, vectors and methods.

BACKGROUND OF THE INVENTION

Endophytes reside in the tissues of living plants and offer aparticularly diverse source of novel compounds and genes that mayprovide important benefits to society, and in particular to agriculture.Endophytes often form mutualistic relationships with their hosts, withthe endophyte conferring increased fitness to the host, often throughthe production of defence compounds. At the same time, the host plantoffers the benefits of a protected environment and nutriment to theendophyte. The plant provides nutrients for the endophyte and a means ofdissemination through the seed. The endophyte protects the host frombiotic (e.g. insect and mammalian herbivory) and abiotic stress (e.g.drought).

Important forage grasses perennial ryegrass and tall fescue are commonlyfound in association with fungal endophytes. Both beneficial anddetrimental agronomic properties result from the association, includingimproved tolerance to water and nutrient stress and resistance to insectpests. Insect resistance is provided by specific metabolites produced bythe endophyte, in particular loline alkaloids and peramine. Othermetabolites produced by the endophyte, lolitrems and ergot alkaloids,are toxic to grazing animals and reduce herbivore feeding. Thesecompounds can accumulate to high levels in plants where they act aspotent feeding deterrents against a range of insect pests.

Janthitrems are a class of indole diterpenes, and are produced by asubgroup of endophytes. In 1980, an outbreak of ryegrass staggerssyndrome led to the first identification of janthitrem alkaloids(Gallagher et al. 1980) Recent discoveries highlight the diversity ofjanthitrems; P. janthinellum isolates from Australia and New Zealandproduce a wide range of janthitrems (janthitrem B, C, D, E, F and G).

Janthitrems are a class of indole diterpenes with structural similarityto lolitrem B (FIG. 1). The epoxy-janthitrems are a group of fivecompounds: three further structures isolated alongside epoxy-janthitremI were assigned epoxy-janthitrem II[10-deacetyl-10,34-(3-methylbut-2-enyl acetal)]; epoxy-janthitrem III[10-deacetyl-34-O-(3-methylbut-2-enyl)]; and epoxy-janthitrem IV[34-O-(3-methylbut-2-enyl)], each of which are derivatives ofepoxy-janthitrem I on the basis of LC-MS analysis. Epoxy-janthitrem I isthe major janthitrem alkaloid produced by perennial ryegrass endophytes.

The presence of janthitrems in perennial ryegrass pastures providessuperior protection against a wide range of important pasture pests.Recent discoveries have indicated that janthitrems can be tremorgenic innature, similar to lolitrem B. Lolitrem B is known to be the maincausative agent in ryegrass staggers. This is a condition in whichanimals grazing on endophyte infected pastures develop ataxia, tremors,and hypersensitivity to external stimuli. Like lolitrem B, janthitrem Bcan induce a tremorgenic response. Recent bioactivity studies ofjanthitrems A and B from P. janthinellum found these two compounds to betremorgenic to mice and to have anti-insect activity to porina (Wiseanacervinata) larvae (Babu, 2009). Further, when purified, Epichloëendophyte derived janthitrems have been observed to exhibitbioprotective properties that provide an advantage to pasture.

Despite these useful properties, janthitrem alkaloids are not wellunderstood when compared to other alkaloid groups synthesised byendophytes. There is an increasing need to further understandjanthitrems and their biosynthesis, as this would provide informationuseful in manipulating janthitrem production.

It is an object of the present invention to overcome, or at leastalleviate, one or more of the difficulties or deficiencies associatedwith the prior art.

SUMMARY OF THE INVENTION

In one aspect, the present invention provides a substantially purifiedor isolated nucleic acid or nucleic acid fragment encoding a geneinvolved in the biosynthesis of a janthitrem in an endophyte.

By ‘nucleic acid’ is meant a chain of nucleotides capable of geneticinformation. The term generally refers to genes or functionally activefragments or variants thereof and or other sequences in the genome ofthe organism that influence its phenotype. The term ‘nucleic acid’includes DNA (such as cDNA or genomic DNA) and RNA (such as mRNA ormicroRNA) that is single- or double stranded, optionally containingsynthetic, non-natural or altered nucleotide bases, synthetic nucleicacids and combinations thereof.

Nucleic acids according to the invention may be full-length genes orpart thereof, and are also referred to as “nucleic acid fragments” and“nucleotide sequences” in this specification. For convenience, theexpression “nucleic acid or nucleic acid fragment” is used to cover allof these.

By ‘substantially purified’ is meant that the nucleic acid is free ofthe genes, which, in the naturally-occurring genome of the organism fromwhich the nucleic acid of the invention is derived, flank the nucleicacid. The term therefore includes, for example, a nucleic acid which isincorporated into a vector; into an autonomously replicating plasmid orvirus; or into the genomic DNA of a prokaryote or eukaryote; or whichexists as a separate molecule (e.g. a cDNA or a genomic or cDNA fragmentproduced by PCR or restriction endonuclease digestion) independent ofother sequences. It also includes a nucleic acid which is part of ahybrid gene encoding additional polypeptide sequence. Preferably, thesubstantially purified nucleic acid is 90%, more preferably 95%, evenmore preferably 98% pure.

The term “isolated” means that the material is removed from its originalenvironment (e.g. the natural environment if it is naturally occurring).For example, a naturally occurring nucleic acid present in a livingplant is not isolated, but the same nucleic acid separated from some orall of the coexisting materials in the natural system, is isolated. Suchnucleic acids could be part of a vector and/or such nucleic acids couldbe part of a composition, and still be isolated in that such a vector orcomposition is not part of its natural environment.

In a preferred embodiment of this aspect of the invention, thejanthitrem producing endophyte is an Epichloë endophyte, in a morepreferred embodiment the endophyte is from the taxa LpTG-3 or LpTG-4,and in an even more preferred embodiment the endophyte is selected fromthe group consisting of NEA12, AR37, 15310, 15311 and E1.

In a second aspect of the present invention there is providedsubstantially purified or isolated nucleic acid or nucleic acid fragmentencoding a janthitrem biosynthesis polypeptide, or complementary orantisense to a sequence encoding a janthitrem biosynthesis polypeptide,said nucleic acid or nucleic acid fragment including a nucleotidesequence selected from the group consisting of (a) sequences shown inFIGS. 7, 10, 13 and 16 hereto (Sequence ID Nos 1, 2, 5, 6, 9, 10, 13 and14);; (b) complements of the sequences recited in (a); (c) sequencesantisense to the sequences recited in (a) and (b); and (d) functionallyactive fragments and variants of the sequences recited in (a), (b) and(c) having at least approximately 80% identity to the relevant part ofthe sequences recited in (a), (b) and (c) and having a size of at least20 nucleotides.

The present invention encompasses functionally active fragments andvariants of the nucleic acids of the present invention. By ‘functionallyactive’ in relation to the nucleic acid is meant that the fragment orvariant (such as an analogue, derivative or mutant) is capable ofmodulating janthitrem biosynthesis. Such variants include naturallyoccurring allelic variants and non-naturally occurring variants.Additions, deletions, substitutions and derivatizations of one or moreof the nucleotides are contemplated so long as the modifications do notresult in loss of functional activity of the fragment or variant.Preferably the functionally active fragment or variant has at leastapproximately 80% identity to the relevant part of the above mentionedsequence to which the fragment or variant corresponds, more preferablyat least approximately 90% identity, even more preferably at leastapproximately 95% identity, most preferably at least approximately 98%identity. Such functionally active variants and fragments include, forexample, those having conservative nucleic acid changes.

Preferably the fragment has a size of at least 20 nucleotides, morepreferably at least 50 nucleotides, more preferably at least 100nucleotides, more preferably at least 200 nucleotides, more preferablyat least 500 nucleotides.

By ‘conservative nucleic acid changes’ is meant nucleic acidsubstitutions that result in conservation of the amino acid in theencoded protein, due to the degeneracy of the genetic code. Suchfunctionally active variants and fragments also include, for example,those having nucleic acid changes which result in conservative aminoacid substitutions of one or more residues in the corresponding aminoacid sequence.

By ‘conservative amino acid substitutions’ is meant the substitution ofan amino acid by another one of the same class, the classes being asfollows:

-   -   Nonpolar: Ala, Val, Leu, Ile, Pro, Met Phe, Trp    -   Uncharged polar: Gly, Ser, Thr, Cys, Tyr, Asn, Gln    -   Acidic: Asp, Glu    -   Basic: Lys, Arg, His

Other conservative amino acid substitutions may also be made as follows:

-   -   Aromatic: Phe, Tyr, His    -   Proton Donor: Asn, Gln, Lys, Arg, His, Trp    -   Proton Acceptor: Glu, Asp, Thr, Ser, Tyr, Asn, Gln

In a further aspect of the present invention, there is provided agenetic construct including a nucleic acid according to the presentinvention. In a preferred embodiment the genetic construct may include achimeric sequence comprising a nucleic acid according to the presentinvention and a gene encoding a mediator or modulator janthitrembiosynthesis. Preferably, the gene encoding a mediator or modulator ofjanthitrem biosynthesis is exogenous, i.e. it does not naturally occurin combination with the nucleic acid according to the present invention.

The term “genetic construct” as used herein refers to an artificiallyassembled or isolated nucleic acid molecule which includes the gene ofinterest. Preferably the genetic construct is a recombinant nucleic acidmolecule. In general a construct may include the gene or genes ofinterest, a marker gene which in some cases can also be the gene ofinterest and appropriate regulatory sequences. Preferably the markergene is exogenous, i.e. it does not naturally occur in combination withthe nucleic acid according to the present invention.

It should be appreciated that the inclusion of regulatory sequences in aconstruct is optional, for example, such sequences may not be requiredin situations where the regulatory sequences of a host cell are to beused. The term construct includes vectors but should not be seen asbeing limited thereto.

By a ‘chimeric sequence’ is meant a hybrid produced by recombinant meansthrough expression of a fusion gene including two or more linked nucleicacids which originally encoded separate proteins, or functionally activefragments or variants thereof.

By a ‘fusion gene’ is meant that two or more nucleic acids are linked insuch a way as to permit expression of the fusion protein, preferably asa translational fusion. This typically involves removal of the stopcodon from a nucleic acid sequence coding for a first protein, thenappending the nucleic acid sequence of a second protein in frame. Thefusion gene is then expressed by a cell as a single protein. The proteinmay be engineered to include the full sequence of both originalproteins, or a functionally active fragment or variant of either orboth.

In a preferred embodiment, the genetic construct according to thepresent invention may be a vector.

The vector may be of any suitable type and may be viral or non-viral.The vector may be an expression vector. Such vectors includechromosomal, non-chromosomal and synthetic nucleic acid sequences, e.g.derivatives of plant viruses; bacterial plasmids; derivatives of the Tiplasmid from Agrobacterium tumefaciens; derivatives of the Ri plasmidfrom Agrobacterium rhizogenes; phage DNA; yeast artificial chromosomes;bacterial artificial chromosomes; binary bacterial artificialchromosomes; vectors derived from combinations of plasmids and phageDNA. However, any other vector may be used as long as it is replicableor integrative or viable in the target cell.

In a preferred embodiment of this aspect of the invention, the geneticconstruct may further include a promoter and a terminator; saidpromoter, gene and terminator being operatively linked.

By a ‘promoter’ is meant a nucleic acid sequence sufficient to directtranscription of an operatively linked nucleic acid sequence.

By ‘operatively linked’ is meant that the nucleic acid(s) and aregulatory sequence, such as a promoter, are linked in such a way as topermit expression of said nucleic acid under appropriate conditions, forexample when appropriate molecules such as transcriptional activatorproteins are bound to the regulatory sequence. Preferably an operativelylinked promoter is upstream of the associated nucleic acid.

By ‘upstream’ is meant in the 3′->5′ direction along the nucleic acid.

The promoter and terminator may be of any suitable type and may beendogenous to the target cell or may be exogenous, provided that theyare functional in the target cell. Preferably, the promoter and/orterminator is exogenous, i.e. it does not naturally occur in combinationwith the nucleic acid according to the present invention.

A variety of terminators which may be employed in the genetic constructsof the present invention are also well known to those skilled in theart. The terminator may be from the same gene as the promoter sequenceor a different gene. Particularly suitable terminators arepolyadenylation signals, such as the (CaMV) 35S polyA and otherterminators from the nopaline synthase (nos) and the octopine synthase(ocs) genes.

The genetic construct, in addition to the promoter, the gene and theterminator, may include further elements necessary for expression of thenucleic acid, in different combinations, for example vector backbone,origin of replication (ori), multiple cloning sites, spacer sequences,enhancers, introns (such as the maize Ubiquitin Ubi intron), antibioticresistance genes and other selectable marker genes [such as the neomycinphosphotransferase (nptll) gene, the hygromycin phosphotransferase (hph)gene, the phosphinothricin acetyltransferase (bar or pat) gene], andreporter genes [such as beta-glucuronidase (GUS) gene (gusA) and thegreen fluorescent protein (GFP) gene (gfp)]. The genetic construct mayalso contain a ribosome binding site for translation initiation. Thegenetic construct may also include appropriate sequences for amplifyingexpression.

Those skilled in the art will appreciate that the various components ofthe genetic construct are operably linked, so as to result in expressionof said nucleic acid. Techniques for operably linking the components ofthe genetic construct of the present invention are well known to thoseskilled in the art. Such techniques include the use of linkers, such assynthetic linkers, for example including one or more restriction enzymesites.

Preferably, the genetic construct is substantially purified or isolated.

By ‘substantially purified’ is meant that the genetic construct is freeof the genes, which, in the naturally-occurring genome of the organismfrom which the nucleic acid or promoter of the invention is derived,flank the nucleic acid or promoter. The term therefore includes, forexample, a genetic construct which is incorporated into a vector; intoan autonomously replicating plasmid or virus; or into the genomic DNA ofa prokaryote or eukaryote; or which exists as a separate molecule (e.g.a cDNA or a genomic or cDNA fragment produced by PCR or restrictionendonuclease digestion) independent of other sequences. It also includesa genetic construct which is part of a hybrid gene encoding additionalpolypeptide sequence.

Preferably, the substantially purified genetic construct is at leastapproximately 90% pure, more preferably at least approximately 95% pure,even more preferably at least approximately 98% pure.

The term “isolated” means that the material is removed from its originalenvironment (e.g. the natural environment if it is naturally occurring).For example, a naturally occurring nucleic acid present in a livingplant is not isolated, but the same nucleic acid separated from some orall of the coexisting materials in the natural system, is isolated. Suchnucleic acids could be part of a vector and/or such nucleic acids couldbe part of a composition, and still be isolated in that such a vector orcomposition is not part of its natural environment.

As an alternative to use of a selectable marker gene to provide aphenotypic trait for selection of transformed host cells, the presenceof the genetic construct in transformed cells may be determined by othertechniques well known in the art, such as PCR (polymerase chainreaction), Southern blot hybridisation analysis, histochemical assays(e.g. GUS assays), thin layer chromatography (TLC), northern and westernblot hybridisation analyses.

The genetic constructs of the present invention may be introduced intoplants or fungi by any suitable technique. Techniques for incorporatingthe genetic constructs of the present invention into plant cells orfungal cells (for example by transduction, transfection, transformationor gene targeting) are well known to those skilled in the art. Suchtechniques include Agrobacterium-mediated introduction,Rhizobium-mediated introduction, electroporation to tissues, cells andprotoplasts, protoplast fusion, injection into reproductive organs,injection into immature embryos and high velocity projectileintroduction to cells, tissues, calli, immature and mature embryos,biolistic transformation, Whiskers transformation, and combinationsthereof. The choice of technique will depend largely on the type ofplant or fungus to be transformed, and may be readily determined by anappropriately skilled person. For transformation of protoplasts,PEG-mediated transformation is particularly preferred. Fortransformation of fungi PEG-mediated transformation and electroporationof protoplasts and Agrobacterium-mediated introduction of hyphalexplants are particularly preferred.

Cells incorporating the genetic constructs of the present invention maybe selected, as described below, and then cultured in an appropriatemedium to regenerate transformed plants or fungi, using techniques wellknown in the art. The culture conditions, such as temperature, pH andthe like, will be apparent to the person skilled in the art. Theresulting plants may be reproduced, either sexually or asexually, usingmethods well known in the art, to produce successive generations oftransformed plants or fungi.

Accordingly, in a further aspect of the present invention there isprovided a transgenic plant cell, plant, plant seed or other plant part,or a transgenic fungus, fungal cell or other fungal part, capable ofproducing janthitrem in greater quantities than an untransformed controlplant cell, plant, plant seed or other plant part, or an untransformedfungus, fungal cell or other fungal part.

In a preferred embodiment the a transgenic plant cell, plant, plant seedor other plant part or the transgenic fungus, fungal cell or otherfungal part has an increase in the quantity of janthitrem produced of atleast approximately 10%, more preferably at least approximately 20%,more preferably at least approximately 30%, more preferably at leastapproximately 40% relative to the untransformed control.

For example, the quantity of janthitrem may be increased by betweenapproximately 10% and 300%, more preferably between approximately 20%and 200%, more preferably between approximately 30% and 100%, morepreferably between approximately 40% and 80% relative to theuntransformed control.

Preferably the transgenic plant cell, plant, plant seed or other plantpart or the transgenic fungus, fungal cell or other fungal part includesa nucleic acid, genetic construct or vector according to the presentinvention. Preferably the transgenic plant cell, plant, plant seed orother plant part, or the transgenic fungus, fungal cell or other fungalpart, is produced by a method according to the present invention.

The present invention also provides a transgenic plant, plant seed orother plant part, or a transgenic fungus, fungal cell or other fungalpart, derived from a plant or fungal cell of the present invention andincluding a nucleic acid, genetic construct or vector of the presentinvention.

The present invention also provides a transgenic plant, plant seed orother plant part, or a transgenic fungus, fungal cell or other fungalpart, derived from a plant or fungus of the present invention andincluding a nucleic acid, genetic construct or vector of the presentinvention.

By ‘plant cell’ is meant any self-propagating cell bounded by asemi-permeable membrane and containing a plastid. Such a cell alsorequires a cell wall if further propagation is desired. Plant cell, asused herein includes, without limitation, algae, cyanobacteria, seedssuspension cultures, embryos, meristematic regions, callus tissue,leaves, roots, shoots, gametophytes, sporophytes, pollen andmicrospores.

By ‘fungal cell’ is meant any cell of a fungus. The term ‘fungus’ refersto whole fungi, fungal organs and tissues (e.g., asci, hyphae,pseudohyphae, rhizoid, sclerotia, sterigmata, spores, sporodochia,sporangia, synnemata, conidia, ascostroma, cleistothecia, mycelia,perithecia, basidia and the like), spores, fungal cells and the progenythereof. Fungi may either exist as single cells or make up amulticellular body called a mycelium, which consists of filaments knownas hyphae. Most fungal cells are multinucleate and have cell walls,composed chiefly of chitin.

By ‘transgenic’ is meant any cell which includes a DNA sequence which isinserted by artifice into a cell and becomes part of the genome of theorganism which develops from that cell.

In a further aspect, the present invention provides a method ofmodifying janthitrem biosynthesis in an endophyte, said method includingintroducing into said endophyte an effective amount of a nucleic acid ornucleic acid fragment or a construct as hereinbefore described. Thepresent invention also provides an endophyte including (e.g. transformedwith) a nucleic acid or nucleic acid fragment or a construct ashereinbefore described. The nucleic acid, nucleic acid fragment orconstruct may be introduced into the endophyte by any suitable method ashereinbefore described.

In a further aspect, the present invention provides a plant inoculatedwith an endophyte as hereinbefore described, said plant comprising anendophyte-free host plant stably infected with said endophyte.Preferably the plant is one in which the endophyte does not naturallyoccur.

Preferably, the plant is infected with the endophyte by a methodselected from the group consisting of inoculation, breeding, crossing,hybridization and combinations thereof.

In a preferred embodiment, the plant may be infected by isogenicinoculation. This has the advantage that phenotypic effects ofendophytes may be assessed in the absence of host-specific geneticeffects. More particularly, multiple inoculations of endophytes may bemade in plant germplasm, and plantlets regenerated in culture beforetransfer to soil.

The identification of an endophyte of the opposite mating-type that ishighly compatible and stable in planta provides a means for molecularbreeding of endophytes for perennial ryegrass. Preferably the plant maybe infected by hyper-inoculation.

Hyphal fusion between endophyte strains of the opposite mating-typeprovides a means for delivery of favourable traits into the host plant,preferably via hyper-inoculation. Such strains are preferably selectedfrom the group including an endophyte strain that exhibits thefavourable characteristics of high inoculation frequency and highcompatibility with a wide range of germplasm, preferably elite perennialryegrass and/or tall fescue host germplasm and an endophyte thatexhibits a low inoculation frequency and low compatibility, but has ahighly favourable alkaloid toxin profile.

It has generally been assumed that interactions between endophyte taxaand host grasses will be species specific. Applicants have surprisinglyfound that endophyte from tall fescue may be used to deliver favourabletraits to ryegrasses, such as perennial ryegrass.

In a further aspect, the present invention provides a plant, plant seedor other plant part derived from a plant of the present invention andstably infected with an endophyte of the present invention.

Preferably, the plant cell, plant, plant seed or other plant part is agrass, more preferably a forage, turf or bioenergy grass, such as thoseof the genera Lolium and Festuca, including L. perenne and L.arundinaceum.

By ‘plant cell’ is meant any self-propagating cell bounded by asemi-permeable membrane and containing plastid. Such a cell alsorequired a cell wall if further propagation is desired. Plant cell, asused herein includes, without limitation, seeds suspension cultures,embryos, meristematic regions, callus tissue, leaves, roots, shoots,gametophytes, sporophytes, pollen and microspores.

In a further aspect, the present invention provides use of an endophyteas hereinbefore described to produce a plant stably infected with saidendophyte.

In a still further aspect, the present invention provides asubstantially purified or isolated polypeptide involved in janthitrembiosynthesis in an endophyte.

In a preferred embodiment, the present invention provides asubstantially purified or isolated janthitrem biosynthesis polypeptideincluding an amino acid sequence selected from the group consisting of(a) sequences shown in FIGS. 8, 11, 14 and 17 (Sequence ID Nos 3, 4, 7,8 11, 12, 15 and 16); and (b) functionally active fragments and variantsof the sequences recited in (a) having at least approximately 80%identity with the relevant part of the sequences recited in (a) andhaving a size of at least 20 amino acids.

The present invention encompasses functionally active fragments andvariants of the polypeptides of the present invention. By ‘functionallyactive’ in this context is meant that the fragment or variant has one ormore of the biological properties of the corresponding protein fromwhich the fragment or variant is derived. Additions, deletions,substitutions and derivatizations of one or more of the amino acids arecontemplated so long as the modifications do not result in loss offunctional activity of the fragment or variant. Preferably the fragmentor variant has at least approximately 80% identity to the relevant partof the above mentioned sequence to which the fragment or variantcorresponds, more preferably at least approximately 90% identity, morepreferably at least approximately 95% identity, most preferably at leastapproximately 98% identity. Such functionally active variants andfragments include, for example, those having conservative amino acidsubstitutions of one or more residues in the corresponding amino acidsequence.

By ‘conservative amino acid substitutions’ is meant the substitution ofan amino acid by another one of the same class, the classes being asfollows:

-   -   Nonpolar: Ala, Val, Leu, Ile, Pro, Met Phe, Trp    -   Uncharged polar: Gly, Ser, Thr, Cys, Tyr, Asn, Gln    -   Acidic: Asp, Glu    -   Basic: Lys, Arg, His

Other conservative amino acid substitutions may also be made as follows:

-   -   Aromatic: Phe, Tyr, His    -   Proton Donor: Asn, Gln, Lys, Arg, His, Trp    -   Proton Acceptor: Glu, Asp, Thr, Ser, Tyr, Asn, Gln

Preferably the fragment has a size of at least 10 amino acids, morepreferably at least 20 amino acids, more preferably at least 50 aminoacids, more preferably at least 100 amino acids, more preferably atleast 200 amino acids.

In a further embodiment of this aspect of the invention, there isprovided a polypeptide recombinantly produced from a nucleic acid ornucleic acid fragment according to the present invention. Techniques forrecombinantly producing polypeptides are known to those skilled in theart.

Availability of the nucleotide sequences of the present invention anddeduced amino acid sequences facilitates immunological screening of cDNAexpression libraries. Synthetic peptides representing portions of theinstant amino acid sequences may be synthesized. These peptides may beused to immunise animals to produce polyclonal or monoclonal antibodieswith specificity for peptides and/or proteins including the amino acidsequences. These antibodies may be then used to screen cDNA expressionlibraries to isolate full-length cDNA clones of interest.

The present invention will now be more fully described with reference tothe accompanying Examples and drawings. It should be understood,however, that the description following is illustrative only and shouldnot be taken in any way as a restriction on the generality of theinvention described above.

BRIEF DESCRIPTION OF THE DRAWINGS/FIGURES

In the Figures:

FIG. 1: Epoxy-janthitrem I and Lolitrem B. Epoxy-janthitrem I is apaxilline-like indole diterpene that exhibits structural similarity tololitrem B. Structure, chemical formula (C39H51NO7) and exact mass(645.3665) of 11,12-epoxyjanthitrem G (epoxy-janthitrem I) from Tapperet al. 2004.

FIG. 2: UPGMA phenogram of genetic relationships among endophytes inryegrass accessions of diverse origins in relation to reference Epichloëspecies. Genetic identity was measured across 18 SSR loci using the Dicecoefficient (Kaur et al, 2015). LpTG-3 and LpTG-4 endophyte strains aregenetically distinct from other asexual Epichloë identified includingEpichloë festucae var. lolii and LpTG-2 (Hettiarachchige et al. 2015).

FIG. 3: Genome survey sequence analysis was used to determine thepresence/absence profiles of the genes responsible for peramine,ergovaline and lolitrem B biosynthesis in endophyte strains representingeach of the four taxa observed to form associations with perennialryegrass (Epichloë festucae var. lolii, LpTG-2, LpTG-3 and LpTG-4).Strains that do not produce lolitrem B have a deletion in the third(ItmE-ItmJ) lolitrem B gene cluster. Adapted from Davidson et al. 2012.

FIG. 4: NEA12 PacBio contig 3 is 247 475 bp in length and has 13predicted and known genes in four clusters. Cluster 1 (ItmG, ItmS, ItmM,ItmK), Cluster 2 (ItmP, ItmQ, ItmF, ItmC, ItmB), Cluster 3 (PP01, PP02)and Cluster 4 (jtmD and jtmO). Light grey arrows display predicted andknown genes and their orientation. The locations of the pks pseudogene,transposase with a MULE domain (PP03), Helitron helicase-liketransposable element (TE), and three AT-rich regions are also shown.PP=predicted protein; TE=transposable element; ip=pseudogene.

FIG. 5: Genomes of representative strains of Epichloë sp. endophytesfrom 4 taxa Epichloë festucae var. lolii (NEA2, NEA6, NEA10), LpTG-2(NEA11), LpTG-3 (N EA 12, AR37, 15310, 15311), LpTG-4 (E1) and FaTG-3(NEA23) were mapped to NEA12 PacBio contig 3. A c. 177436 bp region(c.70039 bp-247475 bp) of the genome unique to janthitrem producing taxaLpTG-3 and LpTG-4 was identified. Within this region there are two geneclusters containing candidate genes (PP01, PP02, jtmD and jtmJ)predicted to be associated with janthitrem biosynthesis in Epichloëendophytes. Endophyte strains from the taxa LpTG-3 and LpTG-4 allcontain candidate genes for janthitrem biosynthesis, while forendophytes from Epichloë festucae var. lolii, LpTG-2 and FaTG-3 thisregion is absent. DNA reads generated using Illumina sequencingtechnology were mapped with Gydle ‘nuclear’ aligner version 3.2.1. Readswere mapped with settings: l 50 (length of overlap); s 25 (sensitivity);k 13 (kmer length); m 6 (maximum number of mis-matches); F 3 (filtersettings). Alignments were visualised with Gydle program Vision version2.6.14 (www.gydle.com).

FIG. 6: In planta expression of NEA12 genome PacBio contig 3 genes.Genomes of representative strains of Epichloë sp. endophytes from LpTG-3(AR37) and Epichloë festucae var. lolii (SE) were mapped to the 247475bp NEA12 PacBio contig 3. In planta expression of candidate genes forjanthitrem biosynthesis in LpTG-3, LpTG-4 and Epichloë festucae var.lolii was determined using RNA-seq analysis of perennialryegrass-endophyte association transcriptome data (refer to key below).DNA and RNA reads were mapped with Gydle ‘nuclear’ aligner(www.gydle.com) version 3.2.1. Reads were mapped with settings: l 50(length of overlap); s 25 (sensitivity); k 13 (kmer length); m 6(maximum number of mis-matches); F 3 (filter settings). Alignments werevisualised with Gydle program Vision version 2.6.14 (www.gydle.com).Expression of Cluster 2 (ItmP, ItmQ, ItmF, ItmC, ItmB), Cluster 1 (ItmG,ItmS, ItmM, ItmK), Cluster 3 (PP01, PP02) and Cluster 4 (jtmD and jtmO)genes was observed for endophyte strains NEA12 and E1 in planta. Cluster3 and Cluster 4 genes are not present in the Epichloë festucae var.lolii (SE) genome, expression of these genes was not observed by SE inplanta.

Key to FIG. 6

Row Genome/Transcriptome Taxon (Strain) Experiment Treatment 1 GenomeLpTG-3 (AR37) genome survey n.a. sequence analysis 2 In planta LpTG-3(NEA12) seedling growth and post imbibition (0 transcriptome maturationhours) 3 In planta LpTG-3 (NEA12) seedling growth and 10 day oldtranscriptome maturation seedlings (10 days) 4 In planta LpTG-4 (E1)transcriptome atlas leaf transcriptome 5 In planta LpTG-4 (E1)transcriptome atlas stigma transcriptome 6 Genome Epichlo{umlaut over(e)} festucae genome survey n.a. var. lolii (SE) sequence analysis 7 Inplanta Epichlo{umlaut over (e)} festucae seedling growth and postimbibition (0 transcriptome var. lolii (SE) maturation hours) 8 Inplanta Epichlo{umlaut over (e)} festucae seedling growth and 10 day oldtranscriptome var. lolii (SE) maturation seedling (10 days)

FIG. 7: Nucleotide sequence for the PP01 gene (Sequence ID No 1). Thecoding sequence for the predicted PP01 protein is highlighted in grey(Sequence ID No 2). The complete nucleotide sequence for the PP01 genewas identified by mapping RNA reads from the in planta (Alto-NEA12)transcriptome data described in FIG. 6 followed by extraction of the DNAsequence from NEA12 PacBio contig 3. Nucleotides shown in lowercase werenot observed in the analysis of the Alto-NEA12 transcriptome dataset.

FIG. 8: PP01 is predicted to be a cytochrome P450 monoxygenase 387 aminoacids in length. Shown here is the alignment of predicted amino acidsequences for PP01 from LpTG-3 strain NEA12 (Sequence ID No 3.) andHirsuteIla minnesotensis (KJZ77225 amino acids 3-379) (Sequence ID No4). Protein identity: 258/387 (66.7%); Protein similarity: 304/387(78.6%); Gaps: 10/387 (2.6%). Sequences were aligned using EMBOSSNeedle.

FIG. 9: Bootstrap consensus tree generated through Maximum Likelihoodanalysis of the predicted amino acid sequence of PP01 from LpTG-3(NEA12) and the top 6 BLASTp hits in the NCBI database. Multiplealignment of complete predicted protein sequences was performed usingClustalW with default parameters. To construct tree topology, maximumlikelihood (ML) was used as implemented in MEGA 6 with defaultparameters and 500 bootstrap replicates. Branches with bootstrap valuesof greater than 70% from 500 bootstrap replications are marked next toeach branch. Genbank accession numbers for each protein sequence isprovided in each tree diagram. PP01 exhibits sequence similarity tocytochrome P450 monoxygenases: KJZ77225.1 [68%; Hirsutella minnesotensis3608]; EQL02233.1 [57%; Ophiocordyceps sinensis CO18]; KND87478.1 [53%;Tolypocladium ophioglossoides CBS 100239]; OAQ66296.1 [50%; Pochoniachlamydosporia 170]; KOM22171.1 [55%; Ophiocordyceps unilateralis];XP_013947710.1 [48%; Trichoderma atroviride IMI 206040].

FIG. 10. Nucleotide sequence for the PP02 gene (Sequence ID No 5). Thecoding sequence for the predicted PP02 protein is highlighted in grey(Sequence ID No 6). Start (ATG) and stop (TGA) codon sequences are shownin bold. Untranslated 5′ and 3′ sequences are shown in lowercase. Thecomplete nucleotide sequence for the PP02 gene was identified by mappingRNA reads from the in planta (Alto-NEA12) transcriptome data describedin FIG. 6 followed by extraction of the DNA sequence from NEA12 PacBiocontig 3.

FIG. 11. PP02 is predicted to be a membrane bound O-acyl transferase(MBOAT) protein 315 amino acids in length. Shown here is the alignmentof predicted amino acid sequences for PP02 from LpTG-3 strain NEA12(Sequence ID No 7) and Oidiodendron maius Zn (KIM95229) (Sequence ID No8). Protein identity: 110/412 (26.7%); Protein similarity: 165/412(40.0%); Gaps: 118/412 (28.6%). Within the predicted MBOAT domain (shownin bold) the two sequences exhibit protein identity of 42% (37/89) andprotein similarity of 61% (54/89). Sequences were aligned using EMBOSSNeedle.

FIG. 12. Bootstrap consensus tree generated through Maximum Likelihoodanalysis of the predicted amino acid sequence of PP02 from LpTG-3(NEA12) and the top 5 BLASTp hits in the NCBI database. Multiplealignment of complete predicted protein sequences was performed usingClustalW with default parameters. To construct tree topology, maximumlikelihood (ML) was used as implemented in MEGA 6 with defaultparameters and 500 bootstrap replicates. Branches with bootstrap valuesof greater than 70% from 500 bootstrap replication are marked next toeach branch. Genbank accession numbers for each protein sequence isprovided in each tree diagram. PP02 exhibits sequence similarity toMBOAT proteins: KIM95229.1 [33%; Oidiodendron maius Zn]; KZL85868.1[30%;Colletotrichum incanum]; CCX05903.1 [30%; Pyronema omphalodes CBS100304]; KZP09605.1 [29%; Fibulorhizoctonia sp. CBS 109695];XP_007593790.1 [31%; Colletotrichum fioriniae PJ7].

FIG. 13. Nucleotide sequence for the jtmD gene (Sequence ID No 9). Thecoding sequence for the predicted JtmD protein is highlighted in grey(Sequence ID No 10). Start (ATG) and stop (TGA) codon sequences areshown in bold. Untranslated 5′ and 3′ sequences are shown in lowercase.The complete nucleotide sequence for the jtmD gene was identified bymapping RNA reads from the in planta (Alto-NEA12) transcriptome datadescribed in FIG. 6 followed by extraction of the DNA sequence fromNEA12 PacBio contig 3.

FIG. 14. JtmD is predicted to be an aromatic prenyl transferase 420amino acids in length (Sequence ID No 11). JtmD exhibits highesthomology to a predicted protein from Ophiocordyceps unilateralis(KOM22681.1) (Sequence ID No 12). Protein identity: 264/420 (62.9%);Protein similarity: 334/420 (79.5%); Gaps: 26/420 (6.2%). Sequences werealigned using EMBOSS Needle.

FIG. 15. Bootstrap consensus tree generated through Maximum Likelihoodanalysis of the predicted amino acid sequence of JtmD from LpTG-3(NEA12) and the top 11 BLASTp hits in the NCBI database. Multiplealignment of complete predicted protein sequences was performed usingClustalW with default parameters. To construct tree topology, maximumlikelihood (ML) was used as implemented in MEGA 6 with defaultparameters and 500 bootstrap replicates. Branches with bootstrap valuesof greater than 70% from 500 bootstrap replication are marked next toeach branch. Genbank accession numbers for each protein sequence isprovided in each tree diagram. JtmD exhibits amino acid sequenceidentity to aromatic prenyl transferases: KOM22681.1 [67%; O.unilateralis]; AGZ20478.1 [49%; P. janthinellum]; AAK11526.2 [46%; P.paxilli]; KOS22745.1 [50%; E. webers]; CEJ54109.1 [47%; P. brasilianum];BAU61555.1 [31%; P. simplicissimum]; AGZ20194.1 [31%; P. crustosum];KZF25225.1 [33%; Xylona heveae TC161]; KGO76903.1 [30%; P. italicum];KJK61458.1 [31%; Aspergillus parasiticus SU-1]; CAP53937.2[[31%;Aspergillus flavus].

FIG. 16. Nucleotide sequence for the jtmO gene (Sequence ID No 13). Thecoding sequence for the predicted JtmO protein is highlighted in grey(Sequence ID No 14). Start (ATG) and stop (TAG) codon sequences areshown in bold. Untranslated 5′ and 3′ sequences are shown in lowercase.The complete nucleotide sequence for the jtmO gene was identified bymapping RNA reads from the in planta (Alto-NEA12) transcriptome datadescribed in FIG. 6 followed by extraction of the DNA sequence fromNEA12 PacBio contig 3.

FIG. 17. JtmO is predicted to be a FAD-binding oxidoreductase 479 aminoacids in length (Sequence ID No 15). JtmO exhibits highest homology to apredicted protein (6-hydroxy-D-nicotine oxidase) from Escovopsis weberi(KOS22754.1) (Sequence ID No 16). Protein identity: 271/481 (56.3%);Protein similarity: 344/481 (71.5%); Gaps: 39/481 (8.1%). Sequences werealigned using EMBOSS Needle.

FIG. 18. Bootstrap consensus tree generated through Maximum Likelihoodanalysis of the predicted amino acid sequence of JtmO from LpTG-3(NEA12) and LpTG-4 (E1) and the top 6 BLASTp hits in the NCBI database.Multiple alignment of complete predicted protein sequences was performedusing ClustalW with default parameters. To construct tree topology,maximum likelihood (ML) was used as implemented in MEGA 6 with defaultparameters and 500 bootstrap replicates. Branches with bootstrap valuesof greater than 70% from 500 bootstrap replication are marked next toeach branch. Genbank accession numbers for each protein sequence isprovided in each tree diagram. JtmO exhibits amino acid sequencesimilarity to FAD-binding oxidoreductases: KOS22754.1 [56%; Escovopsiswebers]; AGZ20488.1 [52%; P. janthinellum]; ADO29935.1 [49%; P.paxilli]; BAU61564.1 [43%; P. simplicissimum]; AGZ20199.1 [43%; P.crustosum]; EON68203.1 [Coniosporium apollinis].

FIG. 19. LC-ESI-FTMS extracted ion chromatogram of metabolites observedin perennial ryegrass- LpTG-3 associations, collected from 0-20 min inpositive ionisation mode (ESI+).

FIG. 20. Proposed pathway for epoxy-janthitrem biosynthesis. Thesuggested scheme follows the indole-diterpene biosynthetic pathway,illustrating a parsimonious route to epoxy-janthitrem I (11,12-epoxjanthitrem G) and its variants (epoxy-janthitrems II-IV). Allmetabolites were observed by LC-MS/MS (FIG. 19).

FIG. 21. Nucleotide sequence of jtmD (Sequence ID No 17). Gene sequencesselected for generation of RNAi silencing vectors are highlighted: Genesequences selected for cassette 2, 3 and 4 are shown in italics(Sequence ID No 18)., underlined (Sequence ID No 19). and in boldrespectively (Sequence ID No 20).

FIG. 22. Schematic diagram of gene silencing vectors. To generate theentry clones, gene cassettes [inverted repeats of candidate genesequences, separated by a 147 bp spacer (cutinase gene intron from M.grisea) and containing attB1 and attB2 sites], were cloned into thepDONR 221 vector using BP clonase (Invitrogen, USA). TheGateway™-enabled destination vector (pEND0002) was constructed throughmodifications of the T-DNA region of pPZP200 containing hph gene(selectable marker) under the control of trpCP (Aspergillus nidulanstryptophan biosynthesis promoter) and trpCT (A. nidulans tryptophanbiosynthesis terminator and first reading frame A [RFA-A] cassette(gateway) under the control of gpdP (A. nidulansglyceraldehyde-3-phosphate dehydrogenase promoter) and trpCT (A.nidulans tryptophan biosynthesis terminator). The final RNA silencingvectors were produced by LR clonase reaction between an entry vector andthe pEND002 vector.

FIG. 23. Fungal protoplast regeneration. A. Regeneration of fungalprotoplasts without hygromycin selection, assessment of protoplastviability. B. Regeneration of fungal protoplasts transformed with RNAsilencing vector on hygromycin selection (arrows indicate individualcolonies). C. Recovery of E1 strains carrying an RNA silencing vector onhygromycin selection.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Identification ofGenes for Janthitrem Biosynthesis in LpTG-3 Endophyte Strain NEA12

Whole genome sequence analysis was used to identify candidate genes forjanthitrem biosynthesis in the NEA12 genome. The protein sequences LtmEand LtmJ from Standard Endophyte (SE) strain were used as querysequences to search the predicted protein database derived from theNEA12 genome. Using this approach, BLASTp searches yielded 13 putativeLtmE protein homologues and 26 putative LtmJ protein homologues in thelibrary of predicted NEA12 proteins.

The NEA12 genome is expected to have predicted LtmE and ItmJ proteinhomologues in common with the SE strain. However, candidates forjanthitrem production would be unique to LpTG-3 and LpTG-4 genomes. AsSE does not produce janthitrems, further analysis was performed toreduce the number of candidates to those present only in LpTG-3 andLpTG-4 endophytes. Each of the 13 putative LtmE protein homologues and26 putative LtmJ protein homologues were used as a BLASTx query of thepredicted SE protein database. A single ItmE NEA12 homologue (g30.t1)was identified in this analysis (Table 1) and therefore the best likelycandidate for further investigation. The predicted protein sequence forgene g30.t1 has homology to aromatic prenyl transferases from P.janthinellum (JanD; 49%) and P. paxilli (PaxD; 46%) (Table 2). Thesegenes are associated with synthesis of the indole diterpenes shearinineK and paxilline respectively. The gene g30.t1 is therefore henceforthreferred to jtmD.

TABLE 1 BLASTx analysis of putative LtmE and LtmJ protein homologuesfrom NEA12 to the SE predicted protein database identified g30.t1 as themost likely candidate gene for janthitrem biosynthesis in NEA12. querysubject % alignment mis- gap q. q. s. s. bit id id identity lengthmatches opens start end start end evalue score g2.t1 g1806.t1 99.75 4031 1 1 403 1 403 0 838 g30.t1 g4103.t1 28.05 385 256 12 22 395 10 3841.00e−37 152 g5701.t1 g6522.t1 86.85 502 25 3 1 483 1 480 0 796 g98.t1g1890.t1 99.4 332 1 1 1 331 1 332 0 678 g7273.t1 g1977.t1 89.06 466 14 31 440 1 455 0 827 g6270.t1 g7010.t1 99.63 537 2 0 1 537 1 537 0 1097

Identification of the Janthitrem Biosynthetic Gene Cluster in the LpTG-3Genome

The NEA12 genome was sequenced using the PacBio Sequel sequencingplatform (PacBio). The contig containing the putative LpTG-3 janthitrembiosynthetic gene cluster was identified using the jtmD gene sequence asa query. The gene content of NEA12 PacBio contig 3 (247 475 kb),containing jtmD, was then annotated using a combination of both Augustus(Stanke and Morgenstern, 2005) gene prediction and manual annotationusing the known gene sequences of LTM genes (Young et al., 2005, 2006)and jtmD (Table 2).

NEA12 PacBio contig 3 contains 13 predicted and known genes (FIG. 4).Cluster 1 (ItmG, ItmS, ItmM, ItmK) and Cluster 2 (ItmP, ItmQ, ItmF,ItmC, ItmB) are located at c. 57243-67332 bp and c. 6838 bp-16951 bprespectively (Table 2). The order and orientation of genes withinCluster 1 and Cluster 2 is maintained as compared to the Epichloëfestucae var. lolli and Epichloë festucae LTM loci (Young et al., 2006;Saikia et al., 2008). Downstream of ItmK, a polyketide synthase (pks)pseudogene (also described by Young et al., 2005), containing severalframe-shift mutations, flanked on the right by an additional AT-richsequence was observed. The topology of the partial LpTG-3 (NEA12) LTMlocus is more similar to that of the Epichloë festucae (FI1) LTM locusthan the Epichloë festucae var. lolli (Lp19) which has tworetrotransposon relics inserted between ItmK and the pks pseudogene(Saikia et al., 2008).

The pks pseudogene defines the left-hand boundary between sequence incommon to LpTG-3 and Epichloë festucae var. lolli (PacBio contig 3: 1bp-c.70039 bp) and a previously undescribed genome sequence unique tojanthitrem producing strains from the taxa LpTG-3 and LpTG-4 (PacBiocontig 3: c.70039 bp-247475 bp) (FIG. 4). The right hand boundary tothis region is defined by the end of PacBio contig 3 (247475 bp). Thisregion of the NEA12 genome is characterised by 4 genes, a transposasewith a MULE domain (159248 bp-163900 bp), a Helitron helicase-liketransposable element (170950 bp-175054 bp), and three AT-rich regions(FIG. 5). Two novel gene clusters termed Cluster 3 and Cluster 4, eachcontaining 2 genes, were identified on NEA12 PacBio contig 3 (Table 2;FIG. 4).

The genomes of representative strains of Epichloë sp. endophytes from 4taxa—Epichloë festucae var. lolii (SE, NEA2, NEA6, NEA10), LpTG-2(NEA11), LpTG-3 (NEA12, AR37, 15310, 15311), LpTG-4 (E1) and FaTG-3(NEA23)—were mapped to NEA12 PacBio contig 3. A region unique tojanthitrem producing taxa LpTG-3 and LpTG-4 was identified (PacBiocontig 3: c.70039 bp-247475 bp) while for endophytes from Epichloëfestucae var. lolii, LpTG-2 and FaTG-3 this region was absent (FIG. 5).None of the genes in this region had been previously described inEpichloë endophytes.

TABLE 2 Sequence analysis of genes and other features identified inNEA12 PacBio contig 3. Position in NEA12 PacBio Top BLASTp Hit contig 3(bp) Percent Genbank Gene Gene Predicted Homologous Identity AccessionID start end cluster function gene (aa) Organism No. Reference ItmP 68387843 2 Cytochrome P450 ItmP 100% Epichloë festucae DQ443465 Young et al,monooxygenase var. lolii 2006 ItmQ 9169 11557 2 Cytochrome P450 ItmQ100% Epichloë festucae DQ443465 Young et al, monooxygenase var. lolii2006 ItmF 12830 14082 2 Prenyl transferase ItmF 99% Epichloë festucaeDQ443465 Young et al, var. lolii 2006 ItmC 16001 14888 2 Prenyltransferase ItmC 100% Epichloë festucae DQ443465 Young et al, var. lolii2006 ItmB 16370 16951 2 Integral membrane ItmB 100% Epichloë festucaeDQ443465 Young et al, protein var. lolii 2006 ItmG 57243 58343 1 GGPPsynthase ItmG  99% Epichloë festucae AY742903 Young at al., var. lolii2005 ItmS 59651 60554 1 Integral membrane ItmS 100% Epichloë festucaeAY742903 Young et al., protein var. lolii 2005 ItmM 61702 63348 1FAD-dependent ItmM  99% Epichloë festucae AY742903 Young at al.,monooxygenase var. lolii 2005 ItmK 65270 67332 1 Cytochrome P450 ItmK 99% Epichloë festucae AY742903 Young at al., monooxygenase var. lolii2005 ψpks 68047 69091 — Polyketide synthase  73% Fusarium equisetiALQ32965.1 unpublished (pseudogene) PP01 117514 116031 3 Cytochrome P450hypothetical  68% Hirsutella KJZ77225 Lai et al., monooxygenase proteinminnesotensis 2014 PP02 118533 119536 3 Membrane bound hypothetical  34%Oidiodendron KIM95229 unpublished O-acyl transferase protein maius ZnjtmD 150720 151982 4 Aromatic prenyl hypothetical  68% OphiocordycepsKOM22681 de Bekker transferase protein unilateralis et al., 2015 PP03159248 163900 4 Transposase hypothetical  86% Hirsutella KJZ68513 Lai etal., protein minnesotensis 2014 jtmO 164992 166560 46-hydroxy-D-nicotine hypothetical  59% Escovopsis KOS22754 unpublishedoxidase protein weberi TE 170950 175054 — Transposable  85% HirsutellaKJZ70955 Lai et al., element minnesotensis 2014

Transcript Expression of Genes Located Within PacBio Contig 3

In planta expression of candidate genes for janthitrem biosynthesis inLpTG-3 (NEA12), LpTG-4 (E1) and Epichloë festucae var. lolii (SE) wasdetermined using RNA-seq analysis of perennial ryegrass-endophyteassociation transcriptome data by mapping the reads generated from twoperennial ryegrass-endophyte transcriptome studies to NEA12 PacBiocontig 3 (FIG. 6). In study one, transcriptome analysis was performed tostudy the major changes that occur in host and endophyte transcriptomesduring seedling growth and maturation at six timepoints, from postimbibition (0 hours) to 10 day old seedlings (10 days) (Sawbridge,2016). Transcript expression for genes within NEA12 PacBio contig 3 inperennial ryegrass cultivar Alto-SE and Alto-NEA12 at two time points (0hours and 10 days) is shown here. In study two, a transcriptome atlasderived from distinct tissue types of perennial ryegrass-endophyteassociation Impact-E1 was developed (Cogan et al., 2012). Transcriptexpression for genes within NEA12 PacBio contig 3 in two tissue types,leaf and stigma are shown here.

In addition to the previously defined Cluster 1 and Cluster 2 genes, thegenes proposed to be involved in janthitrem biosynthesis, PP01, PP02,jtmD and jtmO are also expressed. As Cluster 3 and Cluster 4 genes arenot present in the Epichloë festucae var. lolii (SE) genome, expressionof these genes was not observed by SE in planta.

Detailed Description of the Four Gene Clusters on NEA12 PacBio Contig 3

Cluster 1 (LTM1) and Cluster 2 (LTM2)

Core genes for the initial stages of indole-diterpene biosynthesis inEpichloë spp. are present in LpTG-3 endophyte NEA12. Genes ItmG, ItmCand /trnM are predicted to encode a generanyl geranyl diphosphatesynthase, a prenyl transferase and a FAD-dependent monooxygenase with99%, 100%, 99% amino acid sequence identity compared with theirrespective Ltm homologues in Epichloë festucae var. lolii. The predictedprotein product of ItmB (100%), an integral membrane protein, togetherwith ItmM are proposed to catalyse epoxidation and cyclisation of thediterpene skeleton for paspaline biosynthesis. Genes ItmP (100%) andItmQ (100%) encode cytochrome P450 monooxygenases and complete thecollection of 6 genes required for paxilline biosynthesis in Epichloëspp.

Cluster 3 Genes

Cluster 3 (116033 bp -119536 bp) contains 2 genes, predicted gene PP01(predicted protein 1), a putative cytochrome P450 monoxygenase, andPP02, predicted to be a membrane bound O-acyl transferase (MBOAT)protein (Table 2).

PP01

The nucleotide sequence for the PP01 gene is shown in FIG. 7. PP01 showshomology to a putative cytochrome P450 monoxygenase from HirsuteIlaminnesotensis (FIG. 8; KJZ77225.1), an endoparasitic fungi of thesoybean cyst nematode (Heterodera glycines). PP01 may have a role injanthitrem biosynthesis, however, PP01 does not have a homolog in anyother indole-diterpene gene cluster characterized to date. For example,PP01 does not share sequence similarity with previously describedcytochrome P450 monoxygenases (e.g. LtmP, LtmQ/PaxQ/AtmQ, LtmK) involvedin indole-diterpene biosynthesis (FIG. 9). The predicted proteinsequence of PP01 from E1 (LpTG-4) has 1 amino acid difference (at aminoacid 42 D>G) to that of NEA12 (LpTG-3).

PP02

The nucleotide sequence for the PP02 gene is shown in FIG. 10. PP02 ispredicted to be a membrane bound O-acyl transferase (MBOAT) protein(FIG. 11; FIG. 12). The predicted protein sequence of PP02 from E1(LpTG-4) is identical that of NEA12 (LpTG-3). While membrane associated,PP02 is not a transmembrane protein based on prediction analysis withTMHMM.

Cluster 4

Cluster 4 (150720 bp-175051 bp) contains 2 genes, JtmD an aromaticprenyl transferase, and JtmO predicted to encode a FAD-bindingoxidoreductase.

JtmD

The nucleotide sequence for the jtmD gene is shown in FIG. 13. JtmD,predicted to be an aromatic prenyl transferase, exhibits highesthomology to a predicted protein from Ophiocordyceps unilateralis (63%;FIG. 14). The predicted protein sequence for JtmD also has homology toaromatic prenyl transferases such as those from P. janthinellum (JanD;49%) and P. paxilli (PaxD; 46%) (FIG. 15; Nicholson et al., 2015). Thesegenes are associated with synthesis of the indole diterpenes shearinineK and paxilline respectively. The predicted protein sequence of JtmDfrom NEA12 (LpTG-3) is identical that of E1 (LpTG-4).

JtmO

The nucleotide sequence for the jtmO gene is shown in FIG. 16. JtmOexhibits highest homology to a predicted protein (6-hydroxy-D-nicotineoxidase) from Escovopsis weberi (59%; FIG. 17). JtmO also has homologyto JanO, predicted to be a FAD-binding oxidoreductase, associated withsynthesis of shearinines in P. janthinellum (52%; Nicholson et al.,2015). Genes with similar predicted functions have been identified otherindole-diterpene gene clusters (FIG. 18). The JtmO protein product islikely to have a role in the subsequent modification of theindole-diterpene core. The predicted protein sequence of JtmO in NEA12(LpTG-3) and E1 (LpTG-4) is 97.9% identical. The E1 JtmO predictedprotein has a 9 amino acid deletion (aa 12-20) and one amino acid change(T>A at amino acid 326) compared to that of NEA12.

JtmO

The nucleotide sequence for the jtmO gene is shown in FIG. 16. JtmOexhibits highest homology to a predicted protein (6-hydroxy-D-nicotineoxidase) from Escovopsis weberi (59%; FIG. 17). JtmO also has homologyto JanO, predicted to be a FAD-binding oxidoreductase, associated withsynthesis of shearinines in P. janthinellum (52%; Nicholson et al.,2015). Genes with similar predicted functions have been identified otherindole-diterpene gene clusters (FIG. 18). The JtmO protein product islikely to have a role in the subsequent modification of theindole-diterpene core. The predicted protein sequence of JtmO in NEA12(LpTG-3) and E1 (LpTG-4) is 97.9% identical. The E1 JtmO predictedprotein has a 9 amino acid deletion (aa 12-20) and one amino acid change(T>A at amino acid 326) compared to that of NEA12.

JtmD and JtmO have not previously been described in Epichloë endophytes.Homologues of the two genes have been identified in a number ofPenicillium species (e.g. P. janthinellum, P. paxilli, P. crustosum) andare often found located side by side. It is interesting to note that inthe Escovopsis weberi genome (GenBank: LGSR01000002.1), the two genehomologues identified in this study (JtmD: KOS22745.1; JtmO: KOS22754.1)are also found to be adjacent to each other. Escovopsis sp. areparasitic microfungi that rely on other fungi to be their hosts.

Proposed Biosynthetic Pathway for Janthitrem Production

The work described here provides a genetic basis for janthitrembiosynthesis in Epichloë endophytes, specifically LpTG-3 and LpTG-4.While applicant does not wish to be restricted by theory, it is likelythat in addition to these two asexual taxa there is (or once was) atleast one ancestral sexual Epichloë species that synthesisesjanthitrems.

All of the indole-diterpene gene clusters identified to date have a coreset of genes for the synthesis of paspaline, and a suite of additionalgenes that encode multi-functional cytochrome P450 monooxygenases, FADdependent monooxygenases and prenyl transferases that catalyse variousregio- and stereo-specific oxidations on the molecular skeleton togenerate a diversity of indole-diterpene products.

Robust liquid chromatography-mass-spectrometry (LC-MS) approaches wereemployed to targeted key metabolites associated with the biosynthesis ofindole-diterpene alkaloids.

The extracted ion chromatograms of these metabolites, isolated in plantafrom perennial ryegrass-LpTG-3 associations are illustrated in FIG. 19.The observed accurate masses and fragmentation patterns (via LC-MS/MSanalysis) are indicated in Table 3.

While applicant does not wish to be restricted by theory, based on theidentification and fragmentation of these metabolites, we have proposeda framework for the biosynthesis of the epoxy-janthitrems (FIG. 20).Here, we propose that janthitrem biosynthesis is likely to arise fromthe synthesis of paspaline to p-paxitriol by LtmP and LtmQ. JtmD andJtmO are required for the initial biosynthesis of janthitrems, followedby PP01 and PP02. LtmF and LtmK are required for the synthesis of theepoxy-janthitrems II and IV.

TABLE 3 Targeted LC-MS/MS analysis of the proposed metabolitesassociated with the biosynthesis of epoxy-Janthitrem I and itsderivatives (epoxy-Janthitrem II-IV), following the indole-diterpenealkaloid biosynthetic pathway for LpTG-3 endophytes in planta. Toidentify each metabolite, accurate masses (m/z), retention times (RT)and MSn fragmentation data (LC-MS/MS) were acquired in positiveionisation mode [M + H] using a Thermo Fisher Q-Exactive Plus orbitrapmass spectrometer. Accurate mass and MSn fragmentation results werecompared with theoretical masses and fell within the range of 5 ppmdifference (Delta ppm). Chemical Theoretical m/z RT Production: LC-MS/MSFormula Mass Delta Metabolite [M + H] (min) 1 2 3 4 [M + H] [M + H](ppm) Paspaline 422.3034 12.28 130.0651 182.0960 407.2766 C28 H40 O2 N422.3054 −4.7 13-Desoxypaxilline 420.2534 10.69 130.0651 182.0963402.2420 C27 H34 O3 N 420.2533 0.09 Paxilline 436.2482 9.85 130.0650182.0961 346.1795 C27 H34 O4 N 436.2482 −0.15 β-Paxitriol 436.2482 9.67130.0651 182.0960 335.2132 C27 H36 O4 N 438.2639 2.36 Janthitrem E604.3637 10.60 222.1276 280.1694 546.3211 589.3346 C37 H50 O6 N 604.36330.7 Janthitrem F 646.3735 11.24 222.1277 280.1696 588.3320 631.3459 C39H52 O7 N 646.3738 −0.5 Janthitrem G 630.3807 11.19 222.1274 392.1917615.3461 C39 H52 O6 N 630.3789 2.9 Epoxy-janthitrem I 646.3735 11.24222.1277 280.1696 588.3320 631.3459 C39 H52 O7 N 646.3738 −0.5Epoxy-janthitrem II 670.4076 12.41 222.1275 280.1692 612.3676 655.3814C42 H56 O6 N 670.4102 −3.8 Epoxy-janthitrem III 672.423 12.50 222.1274280.1692 614.3833 657.3969 C42 H58 O6 N 672.4259 −4.3 Epoxy-janthitremIV 714.4341 12.52 222.1278 280.1694 656.3934 699.4081 C44 H60 O7 N714.4364 −3.3

Functional Analysis of Candidate Genes Required for Epoxy-Janthitrem IBiosynthesis

RNAi Silencing of the jtmD Gene

Vector Construction

Three candidate gene sequences (95 bp, 129 bp and 432 bp) within jtmDwere selected for design of RNAi silencing vectors (FIG. 21). Togenerate the entry clones, gene cassettes were cloned into the pDONR 221vector. RNA silencing vectors (FIG. 22) were produced by LR clonasereaction between an entry clones and the Gateway™-enabled destinationvector (pEND0002) (Hettiarachchige, 2014).

Isolation of Fungal Protoplasts

Mycelia were harvested, under sterile conditions, by filtration throughlayers of miracloth lining a funnel and washed 3 times with 30 mL ofsterile ddH₂O. Mycelia were washed with 10 mL of OM buffer (1.2MMgSO₄.7H₂O, 10mM Na₂HPO₄, 100 mM NaH₂PO₄.2H₂O, pH 5.8) and transferredto a sterile 250 mL plastic vessel. Freshly prepared 10 mg/mL Glucanex(30 mL) (Sigma Aldrich) in OM was added and incubated for 18 hrs at 30°C. with gentle shaking (80-100 rpm). The glucanex/protoplast solution(30-50 μL) was examined under a microscope to confirm successfuldigestion. Protoplasts were filtered through miracloth in a funnel, into15 mL sterile glass centrifuge tubes (Gentaur, Belgium) and placed onice. Each tube was carefully overlaid with 2 mL of ST buffer (0.6 Msorbitol, 100mM Tris-HCl, pH 8.0) and centrifuged (Beckman coulter,Avanti® J-251) (5000 rpm for 5 min at 4° C.). Following centrifugation,protoplasts formed a white layer between the glucanex solution and STbuffer and this layer was carefully removed. STC buffer (1 M sorbitol,50 mM CaCl₂.2H₂O, 50 mM Tris-HCl, pH 8.0) (5 mL) was added to theprotoplast solution in fresh sterile glass tubes. Samples were gentlyinverted once and centrifuged (5000 rpm for 5 min at 4° C.). Protoplastpellets were pooled with 5 mL of STC buffer and centrifugation wasrepeated (5000 rpm for 5 min at 4° C.) until only one pellet remained.Excess STC buffer was removed, and the final protoplast pellet wasre-suspended in 500 μL of STC buffer. Protoplast concentration wasestimated by diluting protoplasts (1/100 and/or 1/1000 with STC buffer)and counting using a Haemocytometer and microscope. Protoplasts werediluted with STC to 1.25×10⁸ protoplasts/mL.

PEG-Mediated Fungal Protoplast Transformation

Prior to delivery into fungal protoplasts, the three RNA silencingvectors (FIG. 22) were verified by restriction enzyme digestion andSanger sequencing (data not shown). High quality plasmid DNA, suitablefor transformation into fungal protoplasts was produced, usingPureYield™ Plasmid Midiprep System (Promega), according tomanufacturers' instructions. Aliquots (80 μL) of diluted protoplasts(1.25×10⁸ protoplasts/mL) were prepared on ice. To each aliquot, added;2 μL 50 mM spermidine, 5 μL 5 mg/mL heparin (prepared in STC buffer), 10μg plasmid DNA (1 μg/μL, not exceeding 20 μL) and 20 μL 70% (w/v) PEGsolution [70% (w/v) PEG 4000, 10 mM Tris-HCl pH 8.0, 10 mM CaCl₂].Eppendorf tubes were gently mixed and incubated on ice for 30 min.Following the addition of 1.5 mL STC buffer, protoplasts were mixed andcentrifuged (Eppendorf, Centrifuge 5424 R) (5000 rpm for 5 min at 4°C.). The supernatant was removed and protoplasts were resuspended inregeneration medium II (RG II, 500 μL) (304 g/L sucrose, 1 g/L KH₂PO₄, 1g/L NH₄NO₃, 1 g/L NaCl, 0.25 g/L anhydrous MgSO₄, 0.13 g/L CaCl₂.2H₂O, 1g/L yeast extract, 12 g/L dehydrated potato dextrose, 1 g/L peptone, 1g/L acid hydrolysate of casein) and incubated overnight (22° C., dark,45 rpm).

Fungal Protoplast Regeneration

Overnight protoplast solution (200 μL) was incubated with 800 μL 40%(w/v) PEG solution [40% (w/v) PEG 4000, 1M sorbitol, 50mM Tris-HCl pH8.0, 50 mM CaCl₂], at room temperature for 15 min. Molten (50° C.) 0.4%RG II (5 mL) (304 g/L sucrose, 1 g/L KH₂PO₄, 1 g/L NH₄NO₃, 1 g/L NaCl,0.25 g/L anhydrous MgSO₄, 0.13 g/L CaC1₂.2H₂O, 1 g/L yeast extract, 12g/L dehydrated potato dextrose broth, 1 g/L peptone, 1 g/L acidhydrolysate of casein, 4 g/L agarose) containing 100 μL of theprotoplast/PEG mixture was spread evenly across 0.6% RG II agarose petridishes (304 g/L sucrose, 1 g/L KH₂PO₄, 1 g/L NH₄NO₃, 1 g/L NaCl, 0.25g/L anhydrous MgSO₄, 0.13 g/L CaCl₂.2H₂O, 1 g/L yeast extract, 12 g/Ldehydrated potato dextrose broth, 1 g/L peptone, 1 g/L acid hydrolysateof casein, 6 g/L agarose) containing 100 μg/mL hygromycin B.Representative RG II petri dishes were retained without hygromycinoverlay as controls to assess endophyte viability. All petri dishes wereincubated at 22° C. in the dark for 4-6 weeks until regeneration wasobserved (FIG. 23).

Identification of Transformed Fungal Protoplasts

Individual regenerated colonies were transferred onto petri dishescontaining 15% (w/v) potato dextrose agar (PDA) with 100 μg/mLhygromycin selection and incubated (22° C., dark, 10-21 days).Hygromycin resistant colonies were grown in 250 mL sterile culturevessels in PD broth (50 mL) with 100 μg/mL hygromycin (22° C., dark, 150rpm, 10-21 days) and mycelia were harvested, under sterile conditions,by filtration through layers of miracloth lining a funnel and washedwith 30 mL of sterile M9 phosphate buffer (1 g/L NH₄Cl, 11 g/LNa₂HPO₄.7H₂O, 3 g/L KH₂PO₄, 5 g/L NaCl). Washed mycelia was transferredto a Eppendorf tube, lyophilised (24-48 hrs) and DNA extracted usingDNeasy Plant Mini Kit (Qiagen, Germany) according to manufacturers'instructions. Transformed individuals were identified by polymerasechain reaction (PCR) for the hygromycin gene (hph; fwd5′-tgtcgtccatcacagtttgc-3′ (Sequence ID NO 21), rev5′-gcgccgatggtttctacaaa-3′ (Sequence ID NO 22), and/or the candidatejtmD gene fragments [jtmD (95 bp) fwd 5′-gcctttcttcttgcctgtca-3′(Sequence ID NO 23), rev 5′-gaccgcctgtgtgttttgaa-3′ (Sequence ID NO24),; jtmD (129 bp) fwd 5′-cacacagcccaagattgcat-3 (Sequence ID NO 25)',rev 5′-tggaagtctatcgccactgg-3′(Sequence ID NO 26), jtmD (432 bp) fwd5′-ggagttcagtgcatgctcag-3′(Sequence ID NO 27), rev5′-ggcaagaagaaaggctcacc-3′(Sequence ID NO 28), carried by the RNAsilencing vectors. PCR components and cycling conditions using the CFXConnectTM Real-Time PCR detection system (BioRad) [2xFastStart SYBRGreen master mix (Roche), 10 uM forward and reverse primers, 2 μLtemplate DNA, sterile ddH₂0 (V_(T) 10 μL); 95° C. 10 min, (95° C. 30sec, 60° C. 60 sec, 72° C. 30 sec)×40, 60-95° C. (0.5° C. inc.) 5 min].The assay included appropriate positive and negative control DNA.

Finally, it is to be understood that various alterations, modificationsand/or additions may be made without departing from the spirit of thepresent invention as outlined herein.

REFERENCES

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Development of a transcriptome atlas for perennial ryegrass (Loliumperenne L.). In ‘Abstracts 7th International Symposium on MolecularBreeding of Forage and Turf’. July 2012, Salt Lake City, Utah, USA. p.25.

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Young, C. A., Bryant, M. K., Christensen, M. J., Tapper, B. A., Bryan,G. T., Scott, B. (2005) Molecular cloning and genetic analysis of asymbiosis-expressed gene cluster for lolitrem biosynthesis from amutualistic endophyte of perennial ryegrass. Molecular Genetics andGenomics 274 (1): 13-29.

1-16. (canceled)
 17. A substantially purified or isolated nucleic acidor nucleic acid fragment encoding a janthitrem biosynthesis polypeptide,or complementary or antisense to a sequence encoding a janthitrembiosynthesis polypeptide, said nucleic acid or nucleic acid fragmentincluding a nucleotide sequence selected from the group consisting of(a) sequences shown in FIGS. 7, 10, 13 and 16 (Sequence ID Nos 1, 2, 5,6, 9, 10, 13 and 14); (b) complements of the sequences in (a); (c)sequences antisense to the sequences recited in (a) and (b); and (d)functionally active fragments and variants of the sequences recited in(a), (b) and (c) having at least approximately 80% identity to therelevant part of the sequences recited in (a), (b) and (c) and having asize of at least 20 nucleotides.
 18. A nucleic acid or nucleic acidfragment according to claim 17, wherein said functionally activefragments and variants have at least approximately 95% identity to therelevant part of the sequences recited in (a), (b) and (c) and have asize of at least 200 nucleotides.
 19. A nucleic acid or nucleic acidfragment according to claim 18, wherein said nucleic acid or nucleicacid fragment includes a nucleotide sequence shown in FIGS. 7, 10, 13and
 16. 20. A construct including a nucleic acid or nucleic acidfragment according to claim
 17. 21. A construct according to claim 20,wherein said construct is a vector further including a promoter and aterminator, said promoter, nucleic acid or nucleic acid fragment andterminator being operatively linked.
 22. A method of modifyingjanthitrem biosynthesis in an endophyte, said method includingintroducing into said endophyte an effective amount of a substantiallypurified or isolated nucleic acid or nucleic acid fragment encoding ajanthitrem biosynthesis polypeptide, or complementary or antisense to asequence encoding a janthitrem biosynthesis polypeptide, said nucleicacid or nucleic acid fragment including a nucleotide sequence selectedfrom the group consisting of (a) sequences shown in FIGS. 7, 10, 13 and16 (Sequence ID Nos 1, 2, 5, 6, 9, 10, 13 and 14), (b) complements ofthe sequences in (a), (c) sequences antisense to the sequences recitedin (a) and (b), and (d) functionally active fragments and variants ofthe sequences recited in (a), (b) and (c) having at least approximately80% identity to the relevant part of the sequences recited in (a), (b)and (c) and having a size of at least 20 nucleotides or a constructincluding the substantially purified or isolated nucleic acid or nucleicacid fragment.
 23. A plant inoculated with an endophyte, said plantcomprising an endophyte-free host plant stably infected with saidendophyte, wherein said endophyte has introduced into it an effectiveamount of a substantially purified or isolated nucleic acid or nucleicacid fragment encoding a janthitrem biosynthesis polypeptide, orcomplementary or antisense to a sequence encoding a janthitrembiosynthesis polypeptide, said nucleic acid or nucleic acid fragmentincluding a nucleotide sequence selected from the group consisting of(a) sequences shown in FIGS. 7, 10, 13 and 16 (Sequence ID Nos 1, 2, 5,6, 9, 10, 13 and 14), (b) complements of the sequences in (a), (c)sequences antisense to the sequences recited in (a) and (b), and (d)functionally active fragments and variants of the sequences recited in(a), (b) and (c) having at least approximately 80% identity to therelevant part of the sequences recited in (a), (b) and (c) and having asize of at least 20 nucleotides or a construct including thesubstantially purified or isolated nucleic acid or nucleic acidfragment.
 24. A plant, plant seed or other plant part derived from aplant according to claim 23 and stably infected with the endophyte. 25.Use of an endophyte to produce a plant stably infected with saidendophyte, wherein said endophyte has introduced into it an effectiveamount of a substantially purified or isolated nucleic acid or nucleicacid fragment encoding a janthitrem biosynthesis polypeptide, orcomplementary or antisense to a sequence encoding a janthitrembiosynthesis polypeptide, said nucleic acid or nucleic acid fragmentincluding a nucleotide sequence selected from the group consisting of(a) sequences shown in FIGS. 7, 10, 13 and 16 (Sequence ID Nos 1, 2, 5,6, 9, 10, 13 and 14), (b) complements of the sequences in (a), (c)sequences antisense to the sequences recited in (a) and (b), and (d)functionally active fragments and variants of the sequences recited in(a), (b) and (c) having at least approximately 80% identity to therelevant part of the sequences recited in (a), (b) and (c) and having asize of at least 20 nucleotides or a construct including thesubstantially purified or isolated nucleic acid or nucleic acidfragment.
 26. A substantially purified or isolated polypeptide involvedin janthitrem biosynthesis in an endophyte.
 27. A polypeptide accordingto claim 26, wherein said endophyte is from the taxa LPTG-3 or LPTG-4.28. A substantially purified or isolated janthitrem biosynthesispolypeptide including an amino acid sequence selected from the groupconsisting of (a) sequences shown in FIGS. 8, 11, 14 and 17 (Sequence IDNos 3, 4, 7, 8 11, 12, 15 and 16); and (b) functionally active fragmentsand variants of the sequences recited in (a) having at leastapproximately 80% identity with the relevant part of the sequencesrecited in (a) and having a size of at least 20 amino acids.
 29. Apolypeptide according to claim 28, wherein said functionally activefragments and variants have at least approximately 95% identity to therelevant part of the sequences recited in (a), (b) and (c) and have asize of at least 100 amino acids.